ClinVar Miner

Submissions for variant NM_000038.6(APC):c.6487A>C (p.Lys2163Gln) (rs759728732)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Color RCV000775341 SCV000909613 uncertain significance Hereditary cancer-predisposing syndrome 2018-10-10 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000779713 SCV000916468 uncertain significance not specified 2018-04-13 criteria provided, single submitter clinical testing Variant summary: APC c.6487A>C (p.Lys2163Gln) results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 2.4e-05 in 245562 control chromosomes and is found exclusively in the East Asian subpopulation with MAF of 0.0003480 (6/17242 chr). This frequency is about 5 fold higher than expected for a pathogenic variant in APC causing Familial Adenomatous Polyposis (2.4e-05 vs 7.1e-05), suggesting this variant is possibly a benign polymorphism primarily found in East Asians. c.6487A>C has been reported in the literature in in a Korean gastric cancer patient with co-occurrence of somatic APC variant c.1273delG, and authors classified variant of interest as benign (Kim_2017). However, this report does not provide unequivocal conclusions about an association of the variant with Familial Adenomatous Polyposis. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as VUS-possibly beingn.

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